15-91850865-T-C

Variant names:

• chr15-91850865-T-C
• rs7165398

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.255 in 152,100 control chromosomes in the GnomAD database, including 5,286 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (5286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38795 AN: 151980 Hom.: 5278 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.260

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.255 AC: 38833 AN: 152100 Hom.: 5286 Cov.: 32 AF XY: 0.249 AC XY: 18504 AN XY: 74364

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.259

Alfa AF: 0.241 Hom.: 7258

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7165398; hg19: chr15-92394095;